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TranslatorSRI / Babel

Babel creates cliques of equivalent identifiers across many biomedical vocabularies.
MIT License
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Add GARD #151

Open cbizon opened 1 year ago

cbizon commented 1 year ago

GARD is a rare disease vocabulary, and @newgene needs it in nodenorm to ingest a particular data set.

newgene commented 1 year ago

Thanks @cbizon. The relevant KP source is this new one we added recently:

https://biothings.ncats.io/rare_source

and this relevant issue comment regarding GARD IDs used in this KP API

We will explore a bit to see where we can have a good mapping file for GARD IDs.

cc'ing @erikyao @colleenXu

cbizon commented 1 year ago

It looks like there are lots of mappings in MONDO, so that might be the simplest thing

cc @sierra-moxon in case there's something we should know about the MONDO mappings

newgene commented 1 year ago

:+1: That will be easiest if MONDO already has the mapping.

matentzn commented 1 year ago

Note that GARD has created a new rare disease list they recently supplied to the Mondo team. We have already integrated it into the ETL, so you should see a lot of updated GARD mappings in the next Mondo release cc @nicolevasilevsky

newgene commented 1 year ago

Another related todo item is to add GARD as a supported identifier under BioLink Disease class.

colleenXu commented 1 year ago

we noticed that DOID (disease ontology) seems to have some GARD xrefs? https://disease-ontology.org/?id=DOID:3138

matentzn commented 1 year ago

Note that GARD is undergoing major changes right now - they are compiling a completely new list, which means that many of the old IDs (I counted at least 400, but I may be wrong) are now deprecated.

GARD IDs are derived from ORDO, or in some cases, OMIM. So you can assume that when there is a GARD-ORDO mapping or a GARD-OMIM mapping that is exact as per our SSSOM conversion (https://github.com/monarch-initiative/gard/releases/tag/v2023-06-08, see gard.sssom.tsv), the mapping is 100% correct. That is the safest to use.. For Mondo, in the next release, you will see all the GARD IDs mapped through their ORDO and OMIM associations so when a Mondo ID has an exact ORDO mapping and a GARD ID has that same exact ORDO mapping, the Mondo ID is declared an exact match to the GARD ID).

Because of this, I don't think there is any need to trust a manually curated GARD mapping from any source, since they derived the terms!